A Comprehensive Review of Emerging Approaches in Machine Learning for De Novo PROTAC Design

TL;DR

This review discusses how machine learning techniques are transforming the design of PROTACs, complex molecules used in targeted protein degradation, highlighting recent advances, challenges, and future directions in the field.

Contribution

It provides a comprehensive analysis of ML applications in de novo PROTAC design, emphasizing linker design complexities and evaluating current methodologies and limitations.

Findings

ML accelerates PROTAC development process

Fragment-based drug design informs linker optimization

Current ML methods face challenges in complex PROTAC design

Abstract

Targeted protein degradation (TPD) is a rapidly growing field in modern drug discovery that aims to regulate the intracellular levels of proteins by harnessing the cell's innate degradation pathways to selectively target and degrade disease-related proteins. This strategy creates new opportunities for therapeutic intervention in cases where occupancy-based inhibitors have not been successful. Proteolysis-targeting chimeras (PROTACs) are at the heart of TPD strategies, which leverage the ubiquitin-proteasome system for the selective targeting and proteasomal degradation of pathogenic proteins. As the field evolves, it becomes increasingly apparent that the traditional methodologies for designing such complex molecules have limitations. This has led to the use of machine learning (ML) and generative modeling to improve and accelerate the development process. In this review, we explore the impact of ML on de novo PROTAC design $-$ an aspect of molecular design that has not been comprehensively reviewed despite its significance. We delve into the distinct characteristics of PROTAC linker design, underscoring the complexities required to create effective bifunctional molecules capable of TPD. We then examine how ML in the context of fragment-based drug design (FBDD), honed in the realm of small-molecule drug discovery, is paving the way for PROTAC linker design. Our review provides a critical evaluation of the limitations inherent in applying this method to the complex field of PROTAC development. Moreover, we review existing ML works applied to PROTAC design, highlighting pioneering efforts and, importantly, the limitations these studies face. By offering insights into the current state of PROTAC development and the integral role of ML in PROTAC design, we aim to provide valuable perspectives for researchers in their pursuit of better design strategies for this new modality.